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Poultry Genetics for the Nonprofessional

Brief introduction

The purpose of this document is to provide a poultry genetics reference to
interested poultry enthusiasts who may not have any formal training in
genetics.My personal goal is to provide the enthusiast with
‘the document that I wish I had had when I started poultry
keeping’.

Literature sources are primarily Poultry Breeding and Genetics,
Elsevier 1990, R.D. Crawford, Editor, books by F.P. Jeffrey, W.F. Hollander,
F.B. Hutt and poultry science journals like Poultry Science which are
available in most university libraries. Care is taken to keep the information in
these pages current and to correct any errors.

Part III is a list of chicken genes with comments regarding gene
functions and related information which we hope will be an easy-access reference
for poultry enthusiasts.

I am intentionally avoiding jargon.However, there
are a few basic terms that are necessary.

A gene is a piece of DNA that carries information about a
specific trait.

A chromosome is a string of genes connected together (although
most of the chromosome is DNA that has no known function or no genetic
activity).

An allele is a gene that is a member of a set of genes that all
belong to the same locus, or location, on a chromosome.These
genes are often thought of as being related to each other through mutations (one
allele could be a mutation of another allele) or they could be mutations of an
ancestor gene.

Chickens, like people, usually have two of every
chromosome.The chromosomes in a chromosome pair are not
identical, since one comes from each parent.A gene is said
to be dominant when only one gene (rather than two) is sufficient for the
expression of that trait to which the gene corresponds. Some genes are referred
to as incompletely dominant. The expression of these genes is inhibited
by (usually unknown) modifying genes. When the inhibiting, modifying genes are
not present, the incompletely dominant gene expresses. This interaction with
modifying genes is responsible for the seemingly random nature of the expression
of incompletely dominant genes.

The sex chromosomes are unique in that there are two types, a long sex
chromosome, the Z chromosome, and a short sex chromosome, the W
chromosome.The female has one long and one short sex
chromosome, she has ZW sex chromosomes.The male has two long
sex chromosomes, he has ZZ sex chromosomes.For this reason,
the female has only one copy of some genes that are on the long, Z, sex
chromosome.

The genes that are not on the sex chromosomes are called ‘autosomal’ or
autosomes.Both male and female chickens have two of these
genes.Chickens have 39 pairs of chromosomes (78 individual
chromosomes).Most of them are tiny and referred to as ‘dot’
or micro chromosomes.

An important point is that, when we talk about adding or removing a
gene, say frizzle, F, we don’t intend that the chromosome is lengthened or
shortened by the addition or deletion of that gene.Rather
the frizzle gene, F, replaces the gene of the wild-type jungle fowl,
f+,when it is added, or, it is itself replaced by
the wild-type jungle fowl gene, f+,when frizzle
is removed.I used the frizzle gene as an example here, but
the statement applies to all genes.

The original members of a mating are referred to as the parental
(P) generation. The first generation of progeny from the parental
cross is referred to as the first filial generation, F1. The progeny
of a cross in which one or both of the parents are from the F1 generation
is an F2 generation (F1 x F1 = F2) and so on.

For the interested reader who might like to know the meaning of these
terms, I have included this brief description.A bird that
has one gene, rather than two, for a specific trait is said to be heterozygous
for that trait.A bird that has two genes for a given trait
is homozygous for that trait.The genotype is the actual set
of genes.The phenotype is the appearance or visual
characteristics…what you can see.For example, a bird that is
heterozygous (has one gene instead of two) for a given dominant trait may look
the same as, or similar to, one that is homozygous (has two genes) for that
trait.They both have the same appearance or phenotype.
Because the female fowl have differing sex chromosomes, the long one, Z, and the
short one, W, the Z chromosome has gene locations that the W chromosome does not
(see above). Sometimes when referring to these genes that have no
counterpart on the W chromosome, the female is said to be hemizygous.
Since the female can have only one copy of these genes, there is an
apparent overlap in the meanings of 'heterozygous' and 'hemizygous'.

Both parents have two genes for a given trait.Let’s
consider the gene for frizzle plumage, F, and agree that we will represent the
lack of the frizzle gene with f+.The superscript
‘+’ indicates that the gene is present in the wild-type fowl which, with respect
to chickens, is the red jungle fowl.Here, I apply the jargon
immediately above, but will minimize the use of it from now on.A bird is said to be heterozygous for frizzle if her genotype is (F,
f+) and homozygous if her genotype is (F, F).Since frizzle is dominant, both genotypes will have the same (or similar)
appearance or phenotypes. (In this particular case, frizzle shows a 'dose
effect' and the frizzle homozygote has brittle feathers that usually break off
so the homozygotes can be almost bare. There is a common recessive modifying
factor, mf, that reduces the influence of the frizzle gene.)

To determine the genetics of the offspring, one takes the four possible
combinations of the genes of one parent with the genes of the other
parent.For example, let’s consider a cross between a bird
that has two frizzle genes, homozygous for frizzle, (F, F) and one that is
without frizzle, (f+, f+).It helps
with the bookkeeping for our purposes here if we (artificially) number the
genes: (F1, F2) and (f+1, f+2) so that F1 is the first
frizzle gene of the first parent, F2 is the second frizzle gene of the first
parent and so on.The four possible pairs that can be made by
combining these genes are:(F1, f+1), (F1,
f+2), (F2, f+1) and (F2, f+2).Since frizzle is a dominant trait, these four gene combinations will
result in chickens with frizzle plumage (they will all have the same or
similar phenotypes).In practice one would not number
the genes as I have done in this paragraph.I numbered them
to distinguish the four combinations, since they are all genetically the
same.One would normally write: (F, F) crossed with
(f+, f+) gives (F, f+) times 4.

So, in order to get the four combinations of the genes of the two
parents, just take the first gene of the first pair with each gene of the second
pair, then do the same thing with the second gene of the first pair.The figure below illustrates how to get the combinations of genes of one
parent, (A, B), and the genes of another parent, (C, D).The
four possible combinations are (A, C), (A, D), (B, C) and (B,
D).

Another way to determine the 4 different combinations of the genes for a
trait (two from each parent) is to use a Punnett diagram. In this method one
makes a square that is divided into four quadrants. Write the genes of one
parent across the top with one gene over each quadrant as in the figure below.
Write the genes of the second parent along the left side. In the figure below,
one parent has genes X and Y, while the other parent has genes A and B. This is
a slightly different notation than I used in the previous drawing. Now, in each
quadrant write a gene from each parent. Write the gene from each parent that is
physically nearest the quadrant you are presently working in. Another way to say
this is to put the 'A' gene in the top row of quadrants, the 'B' gene in the
bottom row of quadrants, the 'X' gene in the first column of quadrants and the
'Y' gene in the second column of quadrants. Hopefully the figure below makes
this process clear. The Punnett_Monkey
is an application that will do the Punnett square for you.

Sex-linked traits:

Genes responsible for sex-linked traits are on the long sex chromosome, Z,
but not the short sex chromosome, W.For that reason, I
prefer to use a blank or underscore to represent the missing gene when
representing the genes (genotype) of the female. Some people write a 'W' to
indicate that the presence of the W sex chromosome which lacks the locus for the
gene in question. Rather than writing (B, -) to represent a barred female, some
authors write (B, W) or B/W with the slash separating the gene symbols for the
different chromosomes. I include a clickable link to the
chicken gene tables so the reader can look up the genes that are used in
these examples.

A Punnett diagram (or Punnett square) for determining the mating outcomes
for sex-linked traits is below:

In this example the fact that the female can have only one gene is
represented with a dash or underscore in one column of quadrants. The dash or
underscore actually represents the W chromosome which is what makes her female.
The other gene symbols represent genes that are all allelic to each other (that
means that they all belong to the same location on the chromosome). The chicks
that 'inherit the dash' really inherit the W sex chromosome and are therefore
female. In the example in the Punnett square above, the (A,_) and (B,_) chicks
are the females.

As an example of sex-linked barring (I use it a different way below), the A
and B gene could both represent the wild-type gene, b+, which is lack
of barring. The X gene could represent the barring gene, B. So this is a mating
between a barred female and a nonbarred male. The Punnett square predicts that
all the male chicks will be barred [(B, b+) genotype] and the females
will all be nonbarred [(b+, _) genotype]. Punnett square below is
this mating example (The Punnett_Monkey
is an application that will do the Punnett square for you.):

Saying the same thing a little bit differently, Cuckoo barring or sex-linked
barring, B, is one of these genes that is located on the Z chromosome (recalling
that the male has two Z sex chromosomes and the female has one Z and one W sex
chromosome and there is no barring gene on the W chromosome so females can have
only one).A male with two copies of the barring gene might
be represented as (B, B).This is his ‘genotype’ with respect
to barring.A male with one copy is represented as (B,
b+) where lower-case b+ indicates a lack of the barring
gene and the b+gene is the gene that the wild red jungle fowl has
instead of the barring gene, B.A male with no barring is
represented as (b+, b+).Since the
female has one long chromosome and one short chromosome and the barring gene is
on the long chromosome and not the short one, a female can have only one copy of
the barring gene.A female with barring is represented as (B,
_).A female without barring is represented as
(b+, _).The underscore indicates her short
chromosome lacks the locus (location) of that gene.

I distinguish between the terms ‘sex-linked’ and
‘sex-indicating’.A gene is sex-linked when that gene is on
the long sex chromosome and not the short sex chromosome.A sex-indicating trait is one that arises from a sex-linked gene if
the cross is carried out properly.The following example
indicates this.

When a barred female, (B, _) is crossed with a non-barred male,
(b+, b+), the four possible outcomes (see the figure
above) are:(B, b+), (b+, _), (B,
b+) and (b+, _).Here I have written
all four combinations even though some are the same.The
order of writing the genes of the pair is usually to write the dominant gene
first and the blank last.Of the four possible outcomes, the
males are barred and the females are non-barred.So,
when the cross is carried out this way, barred female x non-barred male, the
barring is a sex-indicating trait, and indicates male offspring.

When a barred male, (B, B) is crossed with a non-barred female,
(b+, _), the four possible combinations of the genes are: (B,
b+), (B, _), (B, b+) and (B, _).Therefore all the chicks will be barred.The barring
is still a sex-linked gene, but the cross was carried out in a way that leads to
both males and females being barred.In this situation the
barring is not indicative of the sex of the offspring.

The Sil-Go-Links (for silver-gold-sex-link) are similar except that the
dominant sex-linked gene is the silver gene, S, which has the function of
inhibiting the red pigment, pheomelanin.The lack of the
silver gene is represented with lower-case s+.Here again, s+ is the gene that the wild-type fowl or red
jungle fowl has instead of the silver gene.Crossing a red
male lacking silver, such as a Rhode Island Red (s+, s+),
with a silver female, such as a Delaware (S, _), gives (S, s+), (S,
s+), (s+, _) and (s+, _).So, the males are silver (which means mostly white) and the females are
red and can be sexed after hatching. Carrying out the cross
the other way, a silver male (S, S) and a red female (s+, _) gives as
possible combinations: (S, s+), (S, s+), (S, _) and (S, _)
so that the red pigment in both males and females is inhibited and they will be
mostly white.

Black sex-links can be made by crossing Barred Rock females with a red male,
such as Rhode Island Red or New Hampshire Red.The Barred
Rock females have one barring gene, (B, _) and should have two nigrum genes (E,
E).The nigrum gene extends black by changing red to
black.The red male will be (b+, b+)
for barring and lacking in nigrum, (e+, e+).Here the lack of nigrum is represented with the symbol, e+,
which indicates that, instead of the nigrum gene, E, the bird has the wild-type
gene that the red jungle fowl has.

With respect to the barring, the four combinations of the genes are: (B,
b+), (B, b+), (b+, _) and (b+,
_).So the males are barred and the females are
not.With respect to the nigrum gene, all four combinations
are the same, (E, e+).So, for this set of genes,
all the chicks will be black and the males will be barred. The
Punnett_Monkey
is an application that will do the Punnett square for you.

How to predict the outcome of a breeding event when two pairs of genes are
involved:

This is relevant in poultry genetics because there are traits that depend on
two or more gene pairs. The Advanced
Punnett_Monkey is an application that allows the user to select as many as
four independent traits and, with a few mouse clicks, determine the frequency,
in percent, that a given genotype will appear in the progeny.The comb type is an example.Shank and foot color are
traits that depend on three pairs of genes.What we do in a
case such as comb type that is determined by two pairs of genes, is to determine
the combinations of the genes of each parent for both sets of genes.We then realize that the combinations of the first genes can occur with
any combination of the second genes.So, we have to consider
all the possible combinations of the genes of the first set with the genes of
the second set.

An example illustrates this.Suppose a trait is determined
by two sets of gene pairs on different chromosomes.A male
with a genes (A, B) and (W, X) for this trait is crossed with a female having
genes (a, b) and (w, x) for the same trait.The possible
combinations from the first gene pair are: (A, a), (A, b), (B, a) and (B,
b).The possible combinations of the second set of genes are:
(W, w), (W, x), (X, w) and (X, x).We’re not finished because
each combination of the first set of genes can occur with any combination of the
second set of genes.To determine these ‘double’ combinations
it is helpful to make a drawing:

The arrows in the figure above indicate the combinations of the (A, a) gene
pair with the four combinations of the second genes: (A, a) with (W, w); (A, a)
with (W, x); (A, a) with (X, w); and (A, a) with (X, x).Next
we do the same thing except using the (A, b) gene pair instead of the (A, a)
one.Then again with the (B, a) gene pair and lastly with the
(B, b) gene pair.This gives 16 ‘double’ combinations.

The inheritance of two sets of gene pairs can be determined by the use of a
Punnett diagram. In these examples, I start with single traits and work with
Punnett diagrams. The strategy is to use Punnett diagrams to
determine the combinations for the single traits separately, then use those
Punnett square combinations to make the larger Punnett square for the
inheritance of both traits together. The Araucana black large fowl is
homozygous for both dominant black, E, and pea comb, P. The Rhode Island Red is
homozygous for recessive wheaten, ey and single comb, p+
(which is really the lack of the pea comb gene). A mating between an Araucana
black large fowl and a Rhode Island Red gives sons and daughters that belong to
the F1 generation and are all heterozygous for dominant black E, recessive
wheaten, ey, P (pea comb) and p+ (lack of pea comb). A
mating between two of these F1 chickens is what I consider here. So, this is
what you would get in the F2 generation.

The F1 sons and daughters are heterozygous for both traits. The F1 fowls are
(E, ey) and (P, p+). Since we know this already, we don't
need to use a Punnett square to determine the distribution of traits in the F1
generation. We do, however, need to use a Punnett square to determine how the
genes combine with each other in the F2 generation (F1 x F1). Then we use a
Punnett square again to determine how the two separate traits appear with each
other. So the Punnett square for first trait has E and ey on both
edges. The other one has P and p+ on both edges. These two Punnett
squares determine how the genes for these traits are inherited separately in the F2 generation from F1 matings. The Punnett
square for the inheritance of the individual traits are:

Now we make another Punnett square to determine how the two traits appear
with each other in the F2 generation. The combinations
from each of these single-trait Punnett squares above is used along an edge of a
new and larger Punnett square to determine how the genes will appear together in
the F2 chickens that come from mating F1 chickens to each other:

The gene combinations that give the same phenotype (appearance) have the
same color in the Punnett square above. So, the F2 generation from a mating of
Araucana and Rhode Island Red will have one fourth that are double heterozygotes
(heterozygous for both traits). These are the four center squares above. This
gene combination occurs four times out of 16, so the percent is 25%. These will
probably be black with a 'poor' pea comb. It may be difficult or impossible to
distinguish them from the EE Pp+ birds. Only 1/16 will be black with
a good, homozygous pea comb (the EE PP combination in the corner).

Because sex-linked traits are popular with fanciers, this next example
considers the inheritance of two sex-linked traits. Consider the cross between a
male that is heterozygous for silver and barring and a female that is red,
non-barred. His genotype is (S, s+) with respect to silver and (B,
b+) for barring. Her genotype is (s+, - ) with respect to
silver and (b+ - ) with respect to barring. First, I make a Punnett
square for the inheritance of the silver trait and another for the barring
trait. I then make another Punnett square with the results of these Punnett
squares.

For the silver trait, the Punnett square is:

The Punnett square for the barring trait is:

The results of these two Punnett diagrams are used to make a larger one.
In the Punnet square below, I have written the results of the Punnett square for
the silver trait across the top and the results of the Punnet square for the
barring trait down the left-hand side. The interior squares of the Punnett
diagram are filled the same way they are for the smaller Punnett diagrams.

Since there are 16 interior squares in this Punnett Diagram, there are 16
possible combinations of the four genes. Because these genes are linked,
the appearance of each combination is not equally probable. See the discussion
of linkage below. If the two traits, silver/gold and barring/non-barring had not
been on the same chromosome, then we could consider each combination in the
Punnett diagram above to be equally probable with the probability being the
number of times a specific combination appears in the Punnett diagram divided by
the number of squares inside the Punnett diagram.

Adding a third gene pair, as one would have to do to consider shank/foot
color (assuming those genes are on different chromosome), is essentially the
same procedure just expanded by a third gene pair.This gives
64 total combinations.

Genes on the same chromosome are ‘linked’and
usually inherited together.Two genes that are always
inherited together would be linked 100% of the time.However,
linkage is never 100% because crossover events occur when the body manufactures
sperm and egg cells.The figure below illustrates a crossover
event.

The two bars on the left side represent two chromosomes having three genes
each.The genes in the middle ‘cross over’ during the process
of sperm or egg cell formation.The end result is that new
‘linkage’ relationships exist for the genes on the chromosomes on the right.

Crossover events are actually very common. The rate of crossover events
occuring between a gene at locus A and a gene at locus B is proportional to the
distance between the two genes on the chromosome (or equivalently, the crossover
rate is proportional to the distance between the two loci). A rule-of-thumb for
the rate of crossover events in poultry is 1% for every 10 map units in
separation between the genes. A map unit is a distance along a chromosome. The
actual distance in length units is not really relevant since all chromosome maps
are written with distance expressed in map units rather than more familiar units
of length.

In the Punnett diagram above describing the gene combinations for two traits,
silver and barring, the loci of the genes are linked because they are both on
the same chromosome, the Z sex chromosome. This means that the wild-type genes,
s+ and b+ genes of the red and non-barred female will be
inherited together most of the time. Occasionally a crossover event will occur
and the genes will be inherited separately. So, while the Punnett square above
gives all the possible combinations of the four genes, it can not be used to
determine the percentages that the gene combinations will appear in the progeny
that arise from a cross between a male that is a heterozygote for silver and
barring and a red, non-barred female.

Since linked genes are inherited together, they can be treated as single
entities in the Punnett square. The Punnett diagram below shows the inheritance
of silver and barring in the mating of a red, non-barred female and a male that
is heterozygous for both barring and silver. This corresponds to the larger
Punnett diagram above, but here I consider that fact that the genes are linked
and I treat them as a single object:

The results of this Punnett square (the gene combinations inside the square)
are what one would get from the mating if no crossover events occurred.
The number of times a given gene combination appears inside the Punnett diagram
divided by the number of squares in the Punnett diagram is the probability or
percent frequency of occurrance of that combination in the progeny. For example,
the males are 50% barred and silver and 50% red and non-barred. The females are
also 50% barred and silver and 50% red and non-barred. The red, barred male
progeny (B b+ s+ s+) that is indicated in the
large Punnett diagram above only occurs when a crossover event has taken place,
if the parents have the genotype we assumed.

This is an important point, namely that we assumed that the barred, silver
male had the B and S genes on the same chromosome. If his genotype had been:
Z1 = B s+ and Z2 = b+ S for his two
Z chromosomes, the red barred male would have been present in the progeny
without requiring a crossover event. The Punnett square for this mating is:

In this mating, half the males are red and barred.
Note from webmaster@Kippenjungle.nl: The genes B and S are more than 50 centiMorgans apart on the Z-chromosome and therefor segregate independantly.

There are varied opinions regarding the issue of inbreeding. One school of
thought contends that inbreeding is a negative thing and brings about depression
in traits such as fertility, hatchability, rate of lay and others. Another
school of thought maintains that the negative aspects of inbreeding can be
controlled and even eliminated to a large extent through intelligent
selection.

Several studies were conducted in the early part of the twentieth century
(for a brief synopsis, see Crawford, Elsevier, 1990, Chapter 39) that showed
essentially disasterous results when full sibling fowl were mated for several
generations. However, even in the first generation of progeny from full sibling
matings in these early studies, traits such as hatchability and rate of lay were
seriously depressed. These early studies are largely responsible for many people
believing that inbreeding in poultry is universally negative.

Other poultry enthusiasts are aware that inbreeding in plants is a very
successful strategy in developing hardy strains with desirable traits. They also
recognize that most lines of show-quality poultry are inbred. Research performed
in the 1970s and later (see Crawford) on inbreeding in chickens (Leghorns),
turkeys, quail, pheasants and partridge fowl showed that desirable traits such
as rate of lay, hatchability and fertility can be selected for in inbred lines.
These traits can recover from the initial depression due to inbreeding,
sometimes even to the same level as the non-inbred lines. A 1988 study by Ameli
and co-workers showed that long-term selection against the negative effects of
inbreeding can be successful in recovering traits such as high rate of lay and
fertility in Leghorn populations.

The depression in traits seen in (random, nonselective) inbreeding, such as
fertility, hatchability and rate of lay, is often due to recessive genes. If the
depression of these traits were due to dominant genes, the depression would be
expressed and observed in non-inbred lines and would not be a phenomenon
associated with inbreeding. Epistasis or Epistacy (the interaction of genes at
different locations on chromosomes) is sometimes invoked to explain aspects of
inbreeding depression.

As of this writing, inbreeding experiments ongoing at the University of
Arkansas have associated the greater part of inbreeding depression on
hatchability to the male. The evidence for this is the following. Inbred females
were mated to a range of different males and the hatchability of their eggs was
observed. Inbred males were bred to a range of different females and the
hatchability of their eggs were observed. The hatchability of eggs from inbred
males was substantially lower than the hatchability of eggs from inbred females,
regardless of the cross. So, for example, the hatchability of eggs from a
father-daughter cross in which the father is an inbred individual was about the
same as the hatchability of eggs from a mating of the same male with non-inbred
females. This is strong evidence that the inbreeding depression of hatchability
is largely a property of the male birds.

The fact remains that, if the backyard fancier allows inbreeding to take
place and does not actively select against the negative effects of inbreeding,
the entire population will perform at a lower level with respect to fertility,
hatchability, rate of lay and and so on. On the other hand, the objective
evidence is convincing that it is possible to develop successful inbred lines of
poultry through active selection for desireable traits.

This presentation of genetics tries to limit the use of jargon.However, the interested reader may well want to participate in
discussions on the Poultry Genetics discussion board, for example, and will need
to know the meanings of some basic terms.Some have already
been defined, but others have not.

In the early stages of the development of the embryo, the cells proliferate
as they must to grow the early embryo, but they remain essentially identical in
that there is no difference among the cells.At a certain
point, cells begin to differentiate into specific tissues.Some make heart and circulatory cells, some make kidneys, liver,
intestines and so on.What controls cell differentiation is
not well understood.

A gamete is the ‘sex cell’.In other words it is
the sperm of the male or the unfertilized egg (ovum) of the female.In general, the gamete has only half the chromosomes of a mature
individual.

Mitosis:There are two types of
cell division processes.One process, mitosis, is the
division of mature cells in the body…cells that have the full compliment of
chromosomes (two pairs of chromosomes).The process of
mitosis has four identifiable phases:

The prophase is an initial organization phase in which the ‘centrioles’
(small centers from which fibers originate…small yellow squares in the figure
above)form and become organized.In the
metaphase spindle fibers emminate from the centrioles and attach to the
chromosomes.The anaphase is characterized by the separation
of the chromosomes by the spindle fibres and the centrioles…they essentially
pull the chromosomes apart.In the telophase the cell wall
closes and new cells are evident.

Meiosis: The process of cell division that produces gametes or
‘sex cells’ (sperm and ovum) .The cells that initiate
meiosis contain the full set of chromosomes.However, the
process of meiosis yields gamete (sperm and ovum) cells that have half that
number of chromosomes.Which chromosomes of the original ones
find their way to the gamete cells is essentially a random process.In this process, the chromosomes (of the chromosome pairs of the parents)
get mixed or ‘scrambled’ in a random fashion.This is also
the point at which crossing over of genes from one chromosome of a chromosome
pair to the other chromosome can occur.